Reproducible

Unlimited

Transparent

Shareable

Complete control and ease of workflow

Automate your commands, e.g. schedule an automatic daily backup

Transparent history

A steeper learning curve, but worth the investment

Open an '.Rproj' with self-contained files

Use the R Studio in-built terminal connected to your Github

Backup straight from R

Cake!

Avoid spaces and CamelCase

• e.g. 'my data.csv', 'My Data.csv' POOR
  
• e.g. 'mydata.csv', 'my_data.csv' GOOD

Annotation

N <- 20 # set rep number  
p <- rep(rnorm(100),N) # repeat a random normal dist of 100 integers N times  

Tab is your friend

change working dir to 'Documents'
cd ~/Documents

move one level up
cd ..

print current working dir
pwd

list files in working dir
ls

make new working dir
mkdir newfolder

create new file
touch text.txt

copy files from source to destination. e.g. cp /Users/mydir/README.txt ~/Documents
cp source destination

copy all folders, subfolders, and files from source to destination
cp -R source destination

move files or folders from source to destination (no need for -R)
mv source destination

move multiple files with the * wildcard, which copies all .rtf files. The tilde (~) symbol is a shortcut for your Home folder, which contains '/Desktop'.
cp ~/Desktop/*.rtf ~/Documents

rename files
mv ~/Desktop/MyFile.rtf ~/Desktop/MyFile-old.rtf
cp ~/Desktop/MyFile.rtf ~/Documents/MyFile-old.rtf

1. Create a repo

2. Create and stage your files

- add and commit your files

3. Push to a remote github repo

- push your files to your Github

Initialise your new local repo

# initialise your local git
git init  

Add the files in your folder to the local git repo

git add . # the '.' adds everything 

Stage the files for the commit

git commit -m 'init commit' # -m adds a message  

We've now added and staged files to a local repo. Version control!

Let's check the changes

git log # recent git activity

git add test.txt # adds individual files  
git status # check what git is doing 

Now we push the changes we made from our local repo to our Github cloud.

1. Create a new Github repo. Name is using best practice, e.g. no spaces
   
2. Don't create a README. Yet.
   

• Uncheck the box 'Initialise this Github with a README'

First, copy the Github repo link you want to push to. Select either https or SSH (requires key access).

Then push your staged (commit) files from your local repo to the remote repo

# set the new remote repo
git remote set-url origin "your github repo"  
# see what remote repositories you have  
git remote -v  
# push changes to remote origin (github) from master branch (local)       
git push origin master 

This creates a git repository on your local machine complete with version control.

Every version of every file for the history of the project is grabbed by default when you run git clone.

git clone "github url" "new repo name (optional)"
# e.g. git clone https://github.com/darwinanddavis/UsefulCode mynewrepo 

local git (version control on your comp)

git init # initialise your local git  
git add . # adds all files to git. replace '.' with filename for individ files
git commit -m 'redo intro' # '-m' = message 

remote git (version control on your github)

# after the above steps ^ 
# see what remote repo you have. if a github one exists, you can just push
git remote -v  
# set the new remote repo (if necessary)  
git remote add origin "your github repo"  # if remote branch doesn't exist
git remote set-url origin "your github repo"  # if already exists
# push changes from local repo to remote repo 
git push -u origin master

If in doubt, ask the internet

fatal: remote origin already exists
The remote origin already exists, so you can't add it again

git remote rm origin # if origin already exists, remove it
git remote add origin "your github repo" # then re-add 
git push origin master # then push again  

! [rejected] master -> master (non-fast-forward) Someone else has made changes since your latest ones and git refuses to lose the commit, so won't push your new changes

git pull origin master # fetches any updates to online repo and merges them    

fatal: refusing to merge unrelated histories Usually associated with a README file on the Github repo

git pull origin master --allow-unrelated-histories # unnecessary parallel history 
# merged to your project. usually associated with a README.md file

If VIM opens, type 'SHIFT + :', then press ENTER

Re-do a commit

git reset --soft HEAD~1

Alternative push option

# option 1
git remote set-url origin "link to existing github repo" # talk to github 
git push -u origin master
# option 2
git remote add github "your github repo"  # if remote branch doesn't exist
git push -u github master

After pushing to your remote repo and this error appears:
! [rejected] master -> master (fetch first)

git fetch origin master # match the local repo commit status to the push destination     
git merge master # merge the recent commits    
git push -u origin master # push to remote repo  

# ------- for non-fast-forward error  ---------
# grab changes made on remote repo and align with local master branch 
git fetch origin master:tmp  
git rebase tmp
git push origin HEAD:master # push the changes from local HEAD to remote    
git branch -D tmp
git push -u origin master # finalise the changes  

For fatal: refusing to merge unrelated histories error

git checkout master
git merge origin/master --allow-unrelated-histories
# or run this before your 'git pull origin master' command  
git pull --allow-unrelated-histories origin master 

Delete files from a Github repo

# ensure you are in the default branch:
git checkout master
# the rm -r command will recursively remove your folder:
git rm -r folder-name
#Commit the change:
git commit -m "Remove duplicated directory"
# push the change to your remote repo
git push origin master

Already on 'master'
M   .Rproj.user/ABE7B653/console06/587CA191
M   .Rproj.user/ABE7B653/sources/prop/INDEX
M   .Rproj.user/shared/notebooks/paths
M   billnye.gif
M   github_presentation.Rmd
M   github_presentation.html
M   installing_git.Rmd
M   installing_git.html
M   installing_git.pdf
M   installing_git.tex
Your branch is up-to-date with 'origin/master'.
fatal: pathspec 'folder-name' did not match any files
On branch master
Your branch is up-to-date with 'origin/master'.
Changes not staged for commit:
    modified:   .Rproj.user/ABE7B653/console06/587CA191
    modified:   .Rproj.user/ABE7B653/sources/prop/INDEX
    modified:   .Rproj.user/shared/notebooks/paths
    modified:   billnye.gif
    modified:   github_presentation.Rmd
    modified:   github_presentation.html
    modified:   installing_git.Rmd
    modified:   installing_git.html
    modified:   installing_git.pdf
    modified:   installing_git.tex

Untracked files:
    R_is_dope.Rmd
    R_is_dope.html
    R_is_dope.pdf
    R_is_dope.tex
    billnye.png
    github_presentation_part2.Rmd
    github_presentation_part2.html

no changes added to commit
Everything up-to-date

If Github questions your user credentials.

git config --global user.email "<your email>" 
git config --global user.name "<your github user name>" 

When using SSH for your github remote repo, e.g. git@github.com:username/reponame.git

Generating a new SSH key

Accessing your SSH key:
- In Mac, in Terminal, type

cat ~/.ssh/id_rsa.pub  

• In Windows, in cmd, type

ls ~/.ssh/*.pub   

How to undo anything with Git

How to access recent commits to your local repo

git log # check recent activity and select commit e.g. 0df4g3 ...  
git checkout "your commit"  
git checkout master  # return to current branch